efb9949075
Former-commit-id: a72f30f90d22cc3c7ff6059e0254e47911bb5af1 Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
127 lines
3.2 KiB
Bash
Executable File
127 lines
3.2 KiB
Bash
Executable File
#!/bin/bash
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#
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#
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#
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# Annotate Organelle
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#
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#========================================================================================
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#
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#
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#========================================================================================
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# -- CAUTION -- Works as long as the script
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# is not called through a symlink
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/scripts/bash_init.sh"
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pushTmpDir ORG.organnot
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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RESULTS=$(basename ${QUERY/.*/})
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LOG="${CALL_DIR}/${RESULTS}.log"
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rm -f ${LOG}
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openLogFile ${LOG}
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loginfo "Normalizing the structure of the Chloroplast sequence..."
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loginfo " LSC + IRB + SSC + IRA"
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${PROG_DIR}/detectors/normalize/bin/go_normalize.sh ${QUERY} > "${RESULTS}.norm.fasta"
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loginfo "Done."
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loginfo "Annotating the Inverted repeats and Single copies (LSC and SSC)..."
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${PROG_DIR}/detectors/ir/bin/go_ir.sh ${QUERY} > "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the tRNA..."
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${PROG_DIR}/detectors/trna/bin/go_trna.sh ${QUERY} >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the rRNA genes..."
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${PROG_DIR}/detectors/rrna/bin/go_rrna.sh ${QUERY} >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Annotating the CDS..."
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${PROG_DIR}/detectors/cds/bin/go_cds.sh ${QUERY} >> "${RESULTS}.annot"
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loginfo "Done."
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loginfo "Printing annotations header..."
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echo "XX"
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echo "FH Key Location/Qualifiers"
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loginfo "Done."
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loginfo "Ordering annotations..."
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awk '/^.....[^ ]/ { \
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match($3,"[0-9][0-9]*"); \
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pos=substr($3,RSTART,RLENGTH)*1000 + 1; \
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print pos,$0} \
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/^..... / { \
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pos++; \
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print pos,$0}' "${RESULTS}.annot" | \
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sort -nk1 | \
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awk '{ \
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match($0,"^[0-9]* ");\
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line=substr($0,RLENGTH+1,100000);\
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print line}'
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loginfo "Done."
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loginfo "Closing annotations table..."
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echo "XX"
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loginfo "Done."
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loginfo "Computing statistics on nucleotide usage..."
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awk '! /^>/ { \
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seq=toupper($0); \
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gsub(" ","",seq); \
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lseq=length(seq); \
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for (i=0; i < lseq; i++) { \
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freq[substr(seq,i,1)]++}\
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} \
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END { \
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other=0; \
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for (i in freq) { \
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if (i!="A" && i!="C" && i!="G" && i!="T") {\
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other+=freq[i] \
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} \
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}; \
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print "SQ Sequence "\
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(freq["A"]+freq["C"]+freq["G"]+freq["T"]+other) \
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" BP; "\
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freq["A"]" A; "\
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freq["C"]" C; "\
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freq["G"]" G; "\
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freq["T"]" T; "\
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other" other;" \
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}' ${QUERY}
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loginfo "Done."
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loginfo "Reformating sequences..."
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lines=$(wc -l ${QUERY} | awk '{print $1}')
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awk -v lines=$lines ' \
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! /^>/ { \
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seq=tolower($0); \
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gsub(" ","",seq); \
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printf(" ") ;\
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for (i=0; i < 6; i++) { \
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f=substr(seq,i * 10, 10); \
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pos+=length(f); \
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f = f substr(" ",1,10-length(f)); \
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printf("%s ",f) \
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}; \
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if (NR==lines) \
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{pos-=1}; \
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printf(" %6d\n",pos) \
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}' ${QUERY}
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loginfo "Done."
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loginfo "Closing sequence part..."
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echo "//"
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loginfo "Done."
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popTmpDir
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